"Now, correct me if I'm wrong, but I thought we went over this whole "implementing an API is a derived work" thing back with Google and Oracle?"
Bukkit isn't a pure API (abstract classes and interfaces). For example, they implemented a permissions system which had no analogue in the base game; all the implementation code is in Bukkit
"after himself and the other core dev basically said they will do whatever they can to prevent Bukkit from continuing."
EvilSeph (the former Bukkit project lead you are referring to) chooses his words very. carefully. indeed. when making a public statement. When he said the project was being shut down he said it was because core developers didn't want to continue. Wolvereness is a core dev, and the lynchpin of the version update process. Given that EvilSeph was very quick to agree that Dinnerbone could continue the project, my instinct is that this started because Wolvereness got fed up and there was no one to fill the void. Wolvereness, however, didn't like the idea that he wasn't indispensible.